Assuming you're correct (which I'm not convinced you are), when you then continue, "I have a checkbox that will make it so they don't track you, but it will also break those sites. Is that ok?" They will also respond "hello no".
Right, because you can easily say that a non-user-triggered window.open() is almost always unwanted. I can't think of any other cases where it's so clear-cut and related to JS, or that disabling a particular facet of JS always would be a net win.
If you're going to claim that there's something like that, provide examples. How do you know people at Mozilla haven't already thought hard about this problem and decided there isn't much more they can do? I bet they have.
> "I have a checkbox that will make it so they don't track you, but it will also break those sites. Is that ok?" They will also respond "hello no".
This overstates the case most of the time because doing this generally breaks relatively little for those domains listed, and to the extent it doesn't, making that decision on a domain-by-domain basis seems to work pretty well (ask any Noscript user)